Well, it sounds like you know some electronics. If it were me I would try to figure out this puzzle myself even though it sounds like you could just get UM to send you a new board.
Attached is the relevant part of the schematic (but the 1.5.6 version but should be the same I would think).
I would examine the circled pin and make sure the logic changes when the X moves left versus right on a long move (long move so there is time to measure the voltage without needing a scope).
The pololu like stepper driver uses the same 2 wires to move left versus right and does so by reversing the voltage across the 2 signals that move the stepper. So I don't think it's likely that the pololu could break in this manner. So I think it must be this "dir" signal (direction). It could be another bad arduino or a bent arduino pin (most likely) or a bad solder on either end of that signal. Or a bent pin on the driver. The driver itself could be bad - this seems very unlikely but easy to test by swapping X driver with any other driver.
later edit: just to be clear - this direction signal should be around 5V (logical high) for one direction of moving and 0V (logical low) for the other direction.
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Checked the Arduino board, the pad was not soldered to the board correctly. I have switched it out for now with another board.
Now I have the system moving only in one directly on X. Stepping + or 0 always moves towards home position.
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